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- EMDB-64188: structure of a 12 base pair Rad51 D-loop complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64188
Titlestructure of a 12 base pair Rad51 D-loop complex
Map data
Sample
  • Complex: mRAD51 D-loop
    • Protein or peptide: DNA repair protein RAD51 homolog 1
    • DNA: DNA (48-MER)
    • DNA: DNA (48-MER)
    • DNA: DNA (35-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
Keywordshomologous recombination / strand exchange / D-loop / RECOMBINATION / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Meiotic recombination / Presynaptic phase of homologous DNA pairing and strand exchange / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) / presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / DNA recombinase assembly ...Meiotic recombination / Presynaptic phase of homologous DNA pairing and strand exchange / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) / presynaptic intermediate filament cytoskeleton / response to glucoside / mitotic recombination-dependent replication fork processing / DNA recombinase assembly / cellular response to camptothecin / chromosome organization involved in meiotic cell cycle / telomere maintenance via telomere lengthening / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / cellular response to cisplatin / cellular response to hydroxyurea / synaptonemal complex / DNA strand exchange activity / replication-born double-strand break repair via sister chromatid exchange / lateral element / regulation of DNA damage checkpoint / telomere maintenance via recombination / single-stranded DNA helicase activity / reciprocal meiotic recombination / regulation of double-strand break repair via homologous recombination / ATP-dependent DNA damage sensor activity / nuclear chromosome / cellular response to alkaloid / replication fork processing / response to X-ray / interstrand cross-link repair / condensed chromosome / DNA polymerase binding / telomere organization / condensed nuclear chromosome / cellular response to ionizing radiation / meiotic cell cycle / male germ cell nucleus / cellular response to gamma radiation / double-strand break repair via homologous recombination / PML body / response to toxic substance / single-stranded DNA binding / site of double-strand break / chromosome / double-stranded DNA binding / chromosome, telomeric region / mitochondrial matrix / response to xenobiotic stimulus / DNA repair / DNA damage response / centrosome / chromatin binding / chromatin / nucleolus / perinuclear region of cytoplasm / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain ...DNA recombination/repair protein Rad51 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA repair protein RAD51 homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsLuo SC / Ho MC
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-TP-113-L01 to M.C.H Taiwan
CitationJournal: To Be Published
Title: Mechanism of strand exchange of eukaryotic homologous recombination from RAD51 D-loop structures
Authors: Luo SC
History
DepositionApr 15, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64188.png

Downloads & links

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Map

FileDownload / File: emd_64188.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.212
Minimum - Maximum-0.6645128 - 1.6989089
Average (Standard dev.)0.0041144 (±0.04562884)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64188_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64188_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mRAD51 D-loop

EntireName: mRAD51 D-loop
Components
  • Complex: mRAD51 D-loop
    • Protein or peptide: DNA repair protein RAD51 homolog 1
    • DNA: DNA (48-MER)
    • DNA: DNA (48-MER)
    • DNA: DNA (35-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: mRAD51 D-loop

SupramoleculeName: mRAD51 D-loop / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: mRAD51 protein filament in complex with dsDNA
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: DNA repair protein RAD51 homolog 1

MacromoleculeName: DNA repair protein RAD51 homolog 1 / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 39.55775 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASWSHPQFE KGADDDDKVP DPMAMQMQLE ASADTSVEEE SFGPQPISRL EQCGINANDV KKLEEAGYHT VEAVAYAPKK ELINIKGIS EAKADKILTE AAKLVPMGFT TATEFHQRRS EIIQITTGSK ELDKLLQGGI ETGSITEMFG EFRTGKTQIC H TLAVTCQL ...String:
MASWSHPQFE KGADDDDKVP DPMAMQMQLE ASADTSVEEE SFGPQPISRL EQCGINANDV KKLEEAGYHT VEAVAYAPKK ELINIKGIS EAKADKILTE AAKLVPMGFT TATEFHQRRS EIIQITTGSK ELDKLLQGGI ETGSITEMFG EFRTGKTQIC H TLAVTCQL PIDRGGGEGK AMYIDTEGTF RPERLLAVAE RYGLSGSDVL DNVAYARGFN TDHQTQLLYQ AEDMMVESRY AL LIVDSAT ALYRTDYSGR GELSARQMHL ARFLRMLLRL ADEFGVAVVI TNQVVAQVDG AAMFAADPKK PIGGNIIAHA STT RLYLRK GRGETRICKI YDSPCLPEAE AMFAINADGV GDAKD

UniProtKB: DNA repair protein RAD51 homolog 1

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Macromolecule #2: DNA (48-MER)

MacromoleculeName: DNA (48-MER) / type: dna / ID: 2 / Details: 3'-tilt dsDNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 14.720452 KDa
SequenceString:
(DC)(DG)(DG)(DT)(DG)(DT)(DC)(DG)(DA)(DG) (DT)(DC)(DA)(DG)(DC)(DC)(DT)(DA)(DT)(DT) (DC)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DA)(DT)(DT)(DC)(DA)(DA)(DT)(DT)(DA) (DA) (DG)(DC)(DA)(DA)(DG)(DT)(DA)(DC)

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Macromolecule #3: DNA (48-MER)

MacromoleculeName: DNA (48-MER) / type: dna / ID: 3 / Details: 5'-tilt dsDNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 14.85651 KDa
SequenceString:
(DG)(DT)(DA)(DC)(DT)(DT)(DG)(DC)(DT)(DT) (DA)(DA)(DT)(DT)(DG)(DA)(DA)(DT)(DG)(DC) (DG)(DT)(DG)(DG)(DG)(DC)(DG)(DA)(DC) (DG)(DT)(DA)(DG)(DG)(DC)(DT)(DG)(DA)(DC) (DT) (DC)(DG)(DA)(DC)(DA)(DC)(DC)(DG)

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Macromolecule #4: DNA (35-MER)

MacromoleculeName: DNA (35-MER) / type: dna / ID: 4
Details: ssDNA, the 3'-end contains extra eight nucleotides (T) that is built based on density map due to end to end fusion of Rad51.
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 10.580766 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DC)(DG)(DT)(DC)(DG)(DC)(DC)(DC) (DA)(DC)(DG)(DC)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)

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Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 9 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 9 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45865
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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